CLI Commands Reference

The attocode code-intel CLI exposes code intelligence features directly from the terminal. All commands work in both local mode (direct filesystem analysis) and remote mode (connected to a running code-intel server).

Quick Reference

Command	Description
query <text>	Semantic search across the codebase
symbols <file>	List symbols in a file or search by name
impact <file> ...	Show blast radius of file changes
hotspots	Show risk/complexity hotspots
deps <file>	Show file dependencies and dependents
gc	Run garbage collection on orphaned data
verify	Run integrity checks on the index
reindex	Force a full reindex of the project

All commands accept --project <path> to specify the project directory (defaults to current directory).

---

Query Commands

query --- Semantic Search

Search across the codebase using natural language. Uses vector similarity + BM25 keyword matching with Reciprocal Rank Fusion.

attocode code-intel query "authentication middleware"
attocode code-intel query "error handling" --top 20
attocode code-intel query "database connection" --filter "*.py"
attocode code-intel query "React hooks" --project /path/to/repo

Flags:

Flag	Default	Description
--top N	10	Number of results to return
--filter GLOB	(none)	File pattern filter (e.g. "*.py", "src/**/*.ts")
--project PATH	.	Project directory

Sample output:

Semantic search: "authentication middleware" (10 results)

  1. [0.92] src/auth/middleware.py
     JWT token validation and session management

  2. [0.87] src/api/security.py
     Request authentication and authorization checks

  3. [0.81] src/auth/oauth.py
     OAuth2 provider integration

---

symbols --- Symbol Listing

List all symbols (functions, classes, methods, variables) in a file, or search for symbols by name across the project.

# List symbols in a file
attocode code-intel symbols src/auth/middleware.py

# Search for a symbol by name
attocode code-intel symbols --search "authenticate"

# Combine with project flag
attocode code-intel symbols src/app.py --project /path/to/repo

Flags:

Flag	Default	Description
--search NAME	(none)	Fuzzy search for symbols by name instead of listing a file
--project PATH	.	Project directory

Sample output (file listing):

Symbols in src/auth/middleware.py

  Kind       Name                          Line
  --------   ---------------------------   ----
  class      AuthMiddleware                  12
  method     AuthMiddleware.__init__         15
  method     AuthMiddleware.dispatch         28
  function   verify_token                    65
  function   extract_bearer                  82
  variable   DEFAULT_REALM                    9

Sample output (search):

Search results for 'authenticate' (5 matches)

  Kind       Name                          File                         Line
  --------   ---------------------------   --------------------------   ----
  function   authenticate_user             src/auth/service.py            34
  method     AuthProvider.authenticate     src/auth/providers/base.py     22
  function   authenticate_request          src/api/security.py            51

---

impact --- Impact Analysis

Show the blast radius of changes to one or more files. Computes transitive dependents to reveal what might break.

attocode code-intel impact src/auth.py
attocode code-intel impact src/auth.py src/config.py
attocode code-intel impact src/core/loop.py --project /path/to/repo

Flags:

Flag	Default	Description
--project PATH	.	Project directory

Sample output:

Impact analysis for 2 file(s):

Changed files:
  src/auth.py
  src/config.py

Direct dependents (depth 1):
  src/api/middleware.py
  src/api/routes/login.py
  src/services/user_service.py

2nd-order dependents (depth 2):
  src/api/app.py
  src/main.py

Total blast radius: 5 files affected

---

hotspots --- Risk Hotspots

Identify files with the highest risk/complexity scores. Scores combine cyclomatic complexity, fan-in/fan-out, file size, and change frequency.

attocode code-intel hotspots
attocode code-intel hotspots --top 20
attocode code-intel hotspots --project /path/to/repo

Flags:

Flag	Default	Description
--top N	15	Number of top hotspots to show
--project PATH	.	Project directory

Sample output:

Code hotspots (top 15 by risk score):

   #  Score  Lines  Fan-in  Fan-out  File
  ---  -----  -----  ------  -------  ----------------------------------------
    1  0.94    3100      28       45  src/agent/agent.py
    2  0.88    1866      15       32  src/core/execution_loop.py
    3  0.82    1233      12       22  src/swarm/swarm_execution.py
    4  0.79    1100       9       18  src/swarm/swarm_orchestrator.py
    5  0.75     990       8       15  src/decomposer/smart_decomposer.py

---

deps --- Dependencies

Show what a file imports and what imports it. Useful for understanding coupling and planning refactors.

attocode code-intel deps src/auth/middleware.py
attocode code-intel deps src/api/app.py --project /path/to/repo

Flags:

Flag	Default	Description
--project PATH	.	Project directory

Sample output:

Dependencies for src/auth/middleware.py

  Imports (this file depends on):
    src/auth/tokens.py
    src/config.py
    src/db/session.py

  Imported by (files that depend on this):
    src/api/app.py
    src/api/routes/admin.py
    src/api/routes/login.py

  Fan-out: 3 | Fan-in: 3

---

Maintenance Commands

gc --- Garbage Collection

Clean up orphaned embeddings, unreferenced content, and stale cache files. Behavior adapts to the deployment mode:

• Local mode: Clears the .attocode/cache directory
• Remote mode: Enqueues gc_orphaned_embeddings and gc_unreferenced_content jobs on the server
• Service mode (with database): Runs GC operations directly against the database

attocode code-intel gc
attocode code-intel gc --project /path/to/repo

Sample output (local):

Local mode: clearing AST cache...
  Removed 47 cached file(s).
GC complete.

Sample output (remote):

Triggering GC on remote server https://code-intel.example.com...
  Enqueued gc_orphaned_embeddings job
  Enqueued gc_unreferenced_content job
GC jobs enqueued on remote server.

---

verify --- Integrity Checks

Run integrity checks on the code-intel index. In local mode, verifies cache and index files exist. In service mode, checks for:

• Orphaned branch_files referencing missing file_contents
• Orphaned embeddings not referenced by any branch manifest
• Missing embeddings for content in branch manifests
• Broken parent_branch_id references
• Orphaned symbols referencing missing file_contents

attocode code-intel verify
attocode code-intel verify --project /path/to/repo

Sample output (service mode, clean):

Running integrity checks...

Integrity check results:
  Orphaned branch_files:      0
  Orphaned embeddings:        0
  Missing embeddings:         0
  Broken parent_branch refs:  0
  Orphaned symbols:           0

All checks passed.

Sample output (with issues):

Running integrity checks...

Integrity check results:
  Orphaned branch_files:      0
  Orphaned embeddings:        12
  Missing embeddings:         3
  Broken parent_branch refs:  0
  Orphaned symbols:           0

Found 2 issue(s):
  [!] 12 embeddings reference content not in any branch manifest
  [!] 3 content SHAs in branch manifests have no embeddings

Run 'attocode code-intel gc' to clean up orphaned data.
Run 'attocode code-intel reindex' to rebuild missing embeddings.

---

reindex --- Full Reindex

Force a complete reindex of the project. Clears all cached data and rebuilds the AST index and embedding vectors from scratch.

• Local mode: Clears cache, removes stale index file, runs full embedding index
• Remote mode: Triggers an index_repository job on the server

attocode code-intel reindex
attocode code-intel reindex --project /path/to/repo

Sample output (local):

Reindexing /path/to/repo...
  Cleared 47 cached file(s).
  Removed stale index file.
  Indexed 1,234 chunks.

Reindex duration

Full reindexing can take several minutes for large projects, depending on file count and embedding model. Use attocode code-intel index --background for non-blocking indexing.